There have been hundreds of studies of the inbred house mouse with experimental infections of tick-borne pathogens, though this model animal is not their natural host. Now, advances in sequencing and bioinformatics mean that forward genetics can be done with the actual hosts for these zoonotic pathogens in nature. These outbred animals have genetic diversity comparable to humans. In North America, Peromyscus leucopus is the prime candidate for this novel approach to understand host responses and adaptations to the tickborne agents of Lyme disease, babesiosis, anaplasmosis, relapsing fever, and Powassan encephalitis. This widely-distributed and abundant rodent species--more closely related to hamsters than to mice or rats--has a long shared evolutionary history with these pathogens. Under these conditions, equilibria develop between pathogens and hosts in terms of virulence of the pathogen and resistance to and tolerance of infection in the mammalian host. The differences in these responses, by pathogen (e.g. bacterial vs. viral) or between individual animals to the same pathogen, offer the opportunity through global expression profiling (this project) and genome-wide association studies (GWAS; long-term goal) for research breakthroughs. These could lead to new diagnostic assays or therapeutic measures that involve key components and pathways of an effective resistance to infection without the consequence of out- of-proportion disease and disability. These studies also have translational implications for those who have proposed transmission-blocking vaccines or CRISPR-based genetic modifications targeting P. leucopus in nature. This developmental two-year project is designed to be hypothesis-generating and to build research infrastructure through development of a new model system and technical capabilities. It leverages our recent success in obtaining a high-quality annotated genome of P. leucopus and preliminary RNA-seq studies. The project entails global expression profiling through genome-wide RNA-seq of animals infected with the agents of Lyme disease and other aforementioned diseases. The subject animals will also be quantitatively phenotyped with regard to traditional and non-traditional parameters, including functional activities, such as working memory. The project's scope and future prospects will be enhanced by establishment at this performance site of a heterogeneous stock colony that is suitable in its diversity and linkage disequilibrium for GWAS. The results of on-going SNP discovery studies will applied for advanced genotyping procedures. The aims are the following: Aim 1: In-depth characterization by quantitative phenotyping measures and by genome-wide RNA-seq of experimental infections of P. leucopus with the agents of Lyme disease, anaplasmosis, babesiosis, hard tick-borne relapsing fever, and Powassan virus encephalitis, as well as a live vaccine based on the vaccinia virus. Aim 2: Establishment at this performance site of a breeding colony of P. leucopus that has the GWAS- favorable genetic diversity and linkage disequilibrium of a long-standing stock colony. Provision of the capacity for genome-wide genotyping of the animals.